[Rdkit-discuss] sanitize mol fail

Thu, 16 Sep 2021 06:23:05 -0700 

Hi all,

I'm trying to read this mol2 file but rdkit fails.
I've read the molecule with sanitize=False, then SanitizeMol, and it raises
this exception: ```AtomKekulizeException: non-ring atom 0 marked aromatic
```

Do you have any how to solve this??

Kind regards,
Eduardo

# created with PyMOL 2.3.1
> @<TRIPOS>MOLECULE
> pdb4k5m.ent_out_ok
> 28 27 1
> SMALL
> USER_CHARGES
> @<TRIPOS>ATOM
> 1   P 13.530 11.826 11.203 P 1 1OV11061O -0.500
> 2  C1 13.172 10.305 17.874 C.cat 1 1OV11061O 0.000
> 3  N1 14.123 9.388 18.088 N.pl3 1 1OV11061O 0.500
> 4  O1 13.434 12.750 10.017 O.2 1 1OV11061O -0.500
> 5  C2 12.314 12.160 16.436 C.3 1 1OV11061O 0.000
> 6  N2 12.126 10.369 18.709 N.2 1 1OV11061O 0.500
> 7  O2 12.755 10.565 10.979 O.2 1 1OV11061O -0.500
> 8  C3 12.699 12.845 15.118 C.3 1 1OV11061O 0.000
> 9  N3 13.288 11.135 16.826 N.2 1 1OV11061O 0.500
> 10  O3 14.957 11.552 11.619 O.2 1 1OV11061O -0.500
> 11  C4 12.784 11.894 13.906 C.3 1 1OV11061O 0.000
> 12  N4 11.286 12.868 12.209 N.4 1 1OV11061O 1.000
> 13  C5 12.694 12.661 12.572 C.3 1 1OV11061O 0.000
> 14 HN3 14.096 11.043 16.227 H 1 1OV11061O 0.000
> 15  H5 13.146 13.643 12.699 H 1 1OV11061O 0.000
> 16 H11 14.914 9.324 17.464 H 1 1OV11061O 0.000
> 17 H12 14.068 8.761 18.879 H 1 1OV11061O 0.000
> 18 H21 12.257 12.902 17.232 H 1 1OV11061O 0.000
> 19 H21 11.400 11.054 18.555 H 1 1OV11061O 0.000
> 20 H22 11.326 11.712 16.347 H 1 1OV11061O 0.000
> 21 H22 12.063 9.752 19.506 H 1 1OV11061O 0.000
> 22 H31 13.638 13.391 15.228 H 1 1OV11061O 0.000
> 23 H32 11.943 13.602 14.918 H 1 1OV11061O 0.000
> 24 H41 11.998 11.138 13.956 H 1 1OV11061O 0.000
> 25 H41 11.257 13.499 11.413 H 1 1OV11061O 0.000
> 26 H42 13.727 11.349 13.967 H 1 1OV11061O 0.000
> 27 H42 10.851 11.987 11.968 H 1 1OV11061O 0.000
> 28 H43 10.775 13.311 12.968 H 1 1OV11061O 0.000
> @<TRIPOS>BOND
> 1 1 4 ar
> 2 1 7 ar
> 3 1 10 ar
> 4 1 13 1
> 5 2 3 ar
> 6 2 6 ar
> 7 2 9 ar
> 8 3 16 1
> 9 3 17 1
> 10 5 8 1
> 11 5 9 1
> 12 5 18 1
> 13 5 20 1
> 14 6 19 1
> 15 6 21 1
> 16 8 11 1
> 17 8 22 1
> 18 8 23 1
> 19 9 14 1
> 20 11 13 1
> 21 11 24 1
> 22 11 26 1
> 23 12 13 1
> 24 12 25 1
> 25 12 27 1
> 26 12 28 1
> 27 13 15 1
> @<TRIPOS>SUBSTRUCTURE
> 1 1OV11061O 1 GROUP 1 **** 1OV1106

Attachment: lig_4k5m.mol2
Description: Binary data

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